Thank you, I had been loading new saved games games without exiting the game. Restarted the mission and it seems to have corrected the problem.
I never liked the retriction of sinking only ships within an area to get credit. An enemy ship carrying material to the UK is as good as any other IMHO and passing up targets to save torpedos for the area sucks in most cases. Guess I will have to live with that even if the real BDU wouldn't bat an eye over it.